Saturday, July 14, 2012

Family Tree DNA Adds New RSRS Reporting for Mitochondrial DNA


STAYING AHEAD OF THE GAME

Family Tree DNA is staying on top of the latest advancements in genetic genealogy, adding a new way of reporting our mitochondrial DNA.
PAPER

In April of this year a paper by Doron Behar (et al) was published proposing a new method of reporting mtDNA. This method uses mutations referenced to a Reconstructed Sapiens Reference Sequence (RSRS) instead of the traditional revised Cambridge Reference Sequence (rCRS). In the author's own words:

In this study, we propose a “Copernican” reassessment of the human mtDNA phylogeny by switching to a Reconstructed Sapiens Reference Sequence (RSRS) as the phylogenetically valid reference point. We aim to trigger the radical but necessary change in the way mtDNA mutations are reported relative to their ancestral/derived status, thus establishing an intellectual cohesiveness with the current consensus of shared common ancestry of all contemporary human mitochondrial genomes.

 NEW RESULTS

In line with this proposal, FTDNA has added the new RSRS values in a tab next to the rCRS values that we are used to seeing.  Here is what it looks like in my account:

rCRS Values (old mutation list)

RSRS Values (new mutation list)

  
IMPROVEMENT OVER rCRS

This new method is an improvement over the old method (based on the 1981 sequence which is now being classified as belonging to the haplogroup H2a2a1), in part, because it uses the root of the tree as the base from which to count mutations rather than the differences from the random sample that has been used in the past. More from the authors:

Mutational events along the human mitochondrial DNA (mtDNA) phylogeny are traditionally identified relative to the revised Cambridge Reference Sequence (rCRS), a contemporary European sequence published in 1981. This historical choice is a continuous source of inconsistencies, misinterpretations and errors in medical, forensic and population genetic studies. Here, after having refined the human mtDNA phylogeny to an unprecedented level by adding information from 8,216 modern mitogenomes, we propose switching the reference to a Reconstructed Sapiens Reference Sequence (RSRS), which was identified by considering all available mitogenomes from Homo neanderthalensis. 

mtDNA Phylogeny - found under "Resources" tab

NEW SITE
 
With this change, FTDNA has also launched a new website:
mtDNACommunity.org is brought to you as a free public service, aiming to facilitate the further understanding of the human mtDNA phylogeny. 

New mtDNA Community Website

Its stated goal is:
This website is committed to the support of the "Copernican" reassessment of the human mtDNA phylogeny and to the establishment of computational tools meant to facilitate phylogenetic analysis and comparison of complete mtDNA sequences. 

It appears that Dr. Behar will be actively involved in the site:

TOOLS TO EASE THE TRANSITION

There are two new tools to help us ease into the transition:
To facilitate data transition from an rCRS to an RSRS based nomenclature we release the tool "FASTmtDNA". Additionally, the tool "mtDNAble" automatically labels haplogroups, performs a phylogeny based quality check and identifies private substitutions. These noted features are fully supported in this website or as standalone versions, which can be freely downloaded from the website including their manual and example files.

MORE DETAILED HAPLOGROUP

On FTDNA's website, I am still listed as haplogroup U5b1, but on mtDNA Community, my full U5b1b2 Haplogroup is reported. That is the same haplogroup reported by 23andMe for me and my matrilineal relatives, so it is nice to see it confirmed here.

More detailed haplogroup

 OUR CITIZEN SCIENTISTS

It is exciting to see that the contributions of genetic genealogists and "citizen scientists" Rebekah Canada and William R. Hurst were acknowledged in this paper and, as we in the genetic genealogy community know, this is well deserved. However, Ian Logan's earlier paper with similar ideas published in 2007 by the Journal of Genetic Genealogy was also deserving of acknowledgement and, perhaps, mistakenly, overlooked.

 MATCHES

Matches can be accessed under the "Community" heading on the new site. I uploaded my results, but I don't have any matches there, so hurry up and add your full sequence so mine isn't so lonely!

**Update - Ann Turner shared the following information in a comment below. I thought it was important enough to add it to the body of this post:
mtDNACommunity is indeed restricted to full mitochondrial sequences. I agree that upgrading would not be informative in terms of finding matches, but you would learn a more detailed haplogroup assignment if that is of interest to you.
All who have tested at 23andMe: you can learn your differences from the RSRS by going to Ancestry Labs / Haplogroup Tree Mutation Mapper. 23andMe doesn't test every position, but all the positions listed will be differences from "mtEve." I did a quick check, and it looks like 73 and 16311 would be the only positions missing along the route between the RSRS and the CRS.
Thanks Ann!
And Bill Hurst (the same William R above) posted on the ISOGG list this new info: FTDNA has listed your "NCBI Number" or GenBank accession number beside your haplogroup designation on your personal page. For me it wasn't there because I submitted to GenBank through Ian Logan, but for anyone who submitted through FTDNA, you should be able to see it. Thanks, Bill!

This is as new to me as it is to the rest of you, so we will learn together as we go. Rebekah Canada has kindly posting an extremely informative "tutorial" on the ISOGG Facebook page, so follow along to learn more.**

12 comments:

  1. Thanks CeCe

    I do have the new RSRS results on my FTDNA profile but when I tried to upload my results to the new website I got the message "The kit number you have entered does not appear to have the Coding Region of mtDNA testing purchased." I don't even have a single mtDNAPlus match so I did not see the point upgrading to the Full Sequence test. Perhaps I can manually input my results.

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    Replies
    1. It sounds like you have HVR1 & HVR2 results. You would have to upgrade to the complete mitoGenome (mtGenome) before taking part in mtDNACommunity.

      I do recommend that for both genealogy and personal ancestry. In the last year, I have seen a few cases of known 5th to 12th cousins be one step off on their mtGenome results.

      Delete
  2. Nope, tried manually and kept getting "Input string was not in a correct format." Tried with and without spaces, with commas vs semi-colons, CRS vs RSRS values.

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  3. CeCe thanks for the update, I was wondering when the system was going to change!

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  4. Helen, mtDNACommunity is indeed retricted to full mitochondrial sequences. I agree that upgrading would not be informative in terms of finding matches, but you would learn a more detailed haplogroup assingment if that is of interest to you.

    All who have tested at 23andMe: you can learn your differences from the RSRS by going to Ancestry Labs / Haplogroup Tree Mutation Mapper. 23andMe doesn't test every position, but all the positions listed will be differences from "mtEve." I did a quick check, and it looks like 73 and 16311 would be the only positions missing along the route between the RSRS and the CRS.

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    Replies
    1. Thanks very much for the clarifications, Ann. mtDNA is your specialty, not mine, so I very much appreciate you sharing your knowledge with all of us here.
      CeCe

      Delete
  5. Thanks Ann, I realized that when I reread this quote above: "This website is committed to the support of the "Copernican" reassessment of the human mtDNA phylogeny and to the establishment of computational tools meant to facilitate phylogenetic analysis and comparison of complete mtDNA sequences."

    I doubt I would learn anything more about my haplogroup by upgrading as it is beyond "special". I have a very rare mutation (16256T) within a rare haplogroup (V). I think FTDNA would have had to test my Coding Region anyway in order to establish a haplogroup for me but have not shared these results with me. Maybe I can use my 23andMe results instead, will try.

    ReplyDelete
    Replies
    1. Hi Helen,

      At FTDNA, your mtDNA Hapogroup based on HVR1 & HVR2 results is assigned using a backbone test. Please see the first two FAQs using this link.
      http://www.familytreedna.com/faq/search.aspx?k=mtdna%20backbone&c=&o=1&ps=25

      :-)

      Rebekah

      Delete
  6. I've uploaded my results. Haplogroup changed from I2 to I2d. Several "private extra" and a few "private missing". I'll keep my ears open to learn more about this.

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  7. For people who have few, if any, mtDNA matches, full mtDNA sequencing may be an especially important action to take -- for those who are interested in further development of their haplogroups. Haplogroup research and development (as shown at Phylotree.com) can only take place when there are adequate numbers of full sequences of a given haplotype that are submitted to GenBank. Further development of many haplogroups is stifled by lack of enough samples.

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  8. Correction: That should be Phylotree.org (not .com)

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